NFI Transcription Factors Interact with FOXA1 to Regulate Prostate-Specific Gene Expression

Abstract

Androgen receptor (AR) action throughout prostate development and in maintenance of the prostatic epithelium is partly controlled by interactions between AR and forkhead box (FOX) transcription factors, particularly FOXA1. We sought to identity additional FOXA1 binding partners that may mediate prostate-specific gene expression. Here we identify the nuclear factor I (NFI) family of transcription factors as novel FOXA1 binding proteins. All four family members (NFIA, NFIB, NFIC, and NFIX) can interact with FOXA1, and knockdown studies in androgen-dependent LNCaP cells determined that modulating expression of NFI family members results in changes in AR target gene expression. This effect is probably mediated by binding of NFI family members to AR target gene promoters, because chromatin immunoprecipitation (ChIP) studies found that NFIB bound to the prostate-specific antigen enhancer. Förster resonance energy transfer studies revealed that FOXA1 is capable of bringing AR and NFIX into proximity, indicating that FOXA1 facilitates the AR and NFI interaction by bridging the complex. To determine the extent to which NFI family members regulate AR/FOXA1 target genes, motif analysis of publicly available data for ChIP followed by sequencing was undertaken. This analysis revealed that 34.4% of peaks bound by AR and FOXA1 contain NFI binding sites. Validation of 8 of these peaks by ChIP revealed that NFI family members can bind 6 of these predicted genomic elements, and 4 of the 8 associated genes undergo gene expression changes as a result of individual NFI knockdown. These observations suggest that NFI regulation of FOXA1/AR action is a frequent event, with individual family members playing distinct roles in AR target gene expression.

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

“…Foxa transcription factors are pioneer factors that interact with NFI in other cell types, and Foxa motifs are enriched around the NFI sites that are more bound in the Nfib high cell lines (Figure S4J) (Grabowska et al 2014). A fraction of sites, therefore, may rely on Foxa factors to maintain a permissive chromatin state around NFI sites, marking them for opening upon Nfib upregulation.…”

Differential impact of RB status on E2F1 reprogramming in human cancer

“…Interestingly, this abbreviated, minimum-affinity E2F motif was found to be enriched in regions of AR binding as well as under epigenetic marks of active transcription (H3K4me3) in recent studies in CRPC tissue (67), suggesting that E2F1 may preferentially interact with AR in CRPC through gained binding capacity at minimum-affinity regions. Moreover, motifs for binding of putative cooperating transcription factors of clinical relevance were enriched in conjunction with gained E2F1 occupancy after RB loss ( Figure 3D), including those associated with: NF1 factors, which can modulate AR function (73,74); TAL-1 (SCL), which influences pioneer factors that modulate AR function (75,76); and the half-site for AR itself. Further, de novo motif analyses additionally implicate AR, as the RB loss-induced E2F1 cistrome was enriched for an AR half-site ( Figure 4C) (77).…”

Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma

“…Recently, recurrent rearrangements involving the MYBL1 gene have been found in gliomas (24, 25), suggesting that it may also be a human oncogene. The NFIB gene also encodes a transcription factor, nuclear factor I/B (NFI-B), a key regulator in hematopoietic and epithelial cells (26, 27), raising the possibility that the MYB - NFIB fusion genes encode novel regulators with the DNA binding domain of c-Myb fused to the specificity and activation domains of NFI-B.…”